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Sengul MY, MacKerell AD. Influence of Mg 2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed Using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling. ACS OMEGA 2023; 8:19532-19546. [PMID: 37305323 PMCID: PMC10249389 DOI: 10.1021/acsomega.3c00931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/11/2023] [Indexed: 06/13/2023]
Abstract
Metal ions, particularly magnesium ions (Mg2+), play a role in stabilizing the tertiary structures of RNA molecules. Theoretical models and experimental techniques show that metal ions can change RNA dynamics and how it transitions through different stages of folding. However, the specific ways in which metal ions contribute to the formation and stabilization of RNA's tertiary structure are not fully understood at the atomic level. Here, we combined oscillating excess chemical potential Grand Canonical Monte Carlo (GCMC) and metadynamics to bias toward the sampling of unfolded states using reaction coordinates generated by machine learning allowing for examination of Mg2+-RNA interactions that contribute to stabilizing folded states of the pseudoknot found in the Twister ribozyme. GCMC is used to sample diverse ion distributions around the RNA with deep learning applied to iteratively generate system-specific reaction coordinates to maximize conformational sampling during metadynamics simulations. Results from 6 μs simulations performed on 9 individual systems indicate that Mg2+ ions play a crucial role in stabilizing the three-dimensional (3D) structure of the RNA by stabilizing specific interactions of phosphate groups or phosphate groups and bases of neighboring nucleotides. While many phosphates are accessible to interactions with Mg2+, it is observed that multiple, specific interactions are required to sample conformations close to the folded state; coordination of Mg2+ at individual specific sites facilitates sampling of folded conformations though unfolding ultimately occurs. It is only when multiple specific interactions occur, including the presence of specific inner-shell cation interactions linking two nucleotides, that conformations close to the folded state are stable. While many of the identified Mg2+ interactions are observed in the X-ray crystal structure of Twister, the present study suggests two new Mg2+ ion sites in the Twister ribozyme that contribute to stabilization. In addition, specific interactions with Mg2+ are observed that destabilize the local RNA structure, a process that may facilitate the folding of RNA into its correct structure.
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Affiliation(s)
- Mert Y. Sengul
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Maryland, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Maryland, Baltimore, Maryland 21201, United States
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2
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Ozernyuk N, Schepetov D. HOX-Gene Cluster Organization and Genome Duplications in Fishes and Mammals: Transcript Variant Distribution along the Anterior–Posterior Axis. Int J Mol Sci 2022; 23:ijms23179990. [PMID: 36077385 PMCID: PMC9456325 DOI: 10.3390/ijms23179990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Hox genes play a crucial role in morphogenesis, especially in anterior–posterior body axis patterning. The organization of Hox clusters in vertebrates is a result of several genome duplications: two rounds of duplication in the ancestors of all vertebrates and a third round that was specific for teleost fishes. Teleostei cluster structure has been significantly modified in the evolutionary processes by Hox gene losses and co-options, while mammals show no such tendency. In mammals, the Hox gene number in a single cluster is stable and generally large, and the numbers are similar to those in the Chondrichthyes. Hox gene alternative splicing activity slightly differs between fishes and mammals. Fishes and mammals have differences in their known alternative splicing activity for Hox gene distribution along the anterior–posterior body axis. The analyzed fish groups—the Coelacanthiformes, Chondrichthyes, and Teleostei—all have higher known alternative mRNA numbers from the anterior and posterior regions, whereas mammals have a more uniform Hox transcript distribution along this axis. In fishes, most Hox transcripts produce functioning proteins, whereas mammals have significantly more known transcripts that do not produce functioning proteins.
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Affiliation(s)
- Nikolay Ozernyuk
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia
- Correspondence:
| | - Dimitry Schepetov
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
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3
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Ye J, Ge L, Geng X, He M, Yang X, Zhang L, Song X. Identification and validation of TCONS_00093333 for regulating fertility conversion of thermo-sensitive cytoplasmic male-sterility wheat with Aegilops kotschyi cytoplasm. Gene X 2022; 838:146707. [DOI: 10.1016/j.gene.2022.146707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/01/2022] [Accepted: 06/24/2022] [Indexed: 11/04/2022] Open
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Brady MM, Meyer AS. Cataloguing the proteome: Current developments in single-molecule protein sequencing. BIOPHYSICS REVIEWS 2022; 3:011304. [PMID: 38505228 PMCID: PMC10903494 DOI: 10.1063/5.0065509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/13/2022] [Indexed: 03/21/2024]
Abstract
The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.
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Affiliation(s)
- Morgan M. Brady
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Anne S. Meyer
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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5
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Kim BH, Woo TG, Kang SM, Park S, Park BJ. Splicing Variants, Protein-Protein Interactions, and Drug Targeting in Hutchinson-Gilford Progeria Syndrome and Small Cell Lung Cancer. Genes (Basel) 2022; 13:genes13020165. [PMID: 35205210 PMCID: PMC8871687 DOI: 10.3390/genes13020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is a biological operation that enables a messenger RNA to encode protein variants (isoforms) that give one gene several functions or properties. This process provides one of the major sources of use for understanding the proteomic diversity of multicellular organisms. In combination with post-translational modifications, it contributes to generating a variety of protein–protein interactions (PPIs) that are essential to cellular homeostasis or proteostasis. However, cells exposed to many kinds of stresses (aging, genetic changes, carcinogens, etc.) sometimes derive cancer or disease onset from aberrant PPIs caused by DNA mutations. In this review, we summarize how splicing variants may form a neomorphic protein complex and cause diseases such as Hutchinson-Gilford progeria syndrome (HGPS) and small cell lung cancer (SCLC), and we discuss how protein–protein interfaces obtained from the variants may represent efficient therapeutic target sites to treat HGPS and SCLC.
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Affiliation(s)
- Bae-Hoon Kim
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
| | - Tae-Gyun Woo
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
| | - Soyoung Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
| | - Bum-Joon Park
- Rare Disease R&D Center, PRG S&T Co., Ltd., Busan 46241, Korea; (B.-H.K.); (T.-G.W.)
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46274, Korea; (S.-M.K.); (S.P.)
- Correspondence:
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6
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Siddika T, Heinemann IU. Bringing MicroRNAs to Light: Methods for MicroRNA Quantification and Visualization in Live Cells. Front Bioeng Biotechnol 2021; 8:619583. [PMID: 33537295 PMCID: PMC7848212 DOI: 10.3389/fbioe.2020.619583] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
MiRNAs are small non-coding RNAs that interact with their target mRNAs for posttranscriptional gene regulation. Finely controlled miRNA biogenesis, target recognition and degradation indicate that maintaining miRNA homeostasis is essential for regulating cell proliferation, growth, differentiation and apoptosis. Increasingly, miRNAs have been recognized as a potential biomarker for disease diagnosis. MiRNAs can be found in blood, plasma, and tissues, and miRNA expression and activity differ in developmental stages, tissues and in response to external stimuli. MiRNA transcripts are matured from pri-miRNA over pre-miRNA to mature miRNA, a process that includes multiple steps and enzymes. Many tools are available to identify and quantify specific miRNAs, ranging from measuring total miRNA, specific miRNA activity, miRNA arrays and miRNA localization. The various miRNA assays differ in accuracy, cost, efficiency and convenience of monitoring miRNA dynamics. To acknowledge the significance and increasing research interest in miRNAs, we summarize the traditional as well as novel methods of miRNA quantification with strengths and limitations of various techniques in biochemical and medical research.
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Affiliation(s)
| | - Ilka U. Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
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7
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The crosstalk between bone metabolism, lncRNAs, microRNAs and mRNAs in coronary artery calcification. Genomics 2020; 113:503-513. [PMID: 32971215 DOI: 10.1016/j.ygeno.2020.09.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/31/2020] [Accepted: 09/19/2020] [Indexed: 01/02/2023]
Abstract
The association between Coronary Artery Calcification (CAC) and osteoporosis has been reported but not fully understood. Therefore, using an original bioinformatic framework we analyzed transcriptomic profiles of 20 elderly women with high CAC score and 31 age- and sex-matching controls from São Paulo Ageing & Health study (SPAH). We integrated differentially expressed microRNA (miRNA) and long-noncoding RNA (lncRNA) interactions with coding genes associated with CAC, in the context of bone-metabolism genes mined from literature. Top non-coding regulators of bone metabolism in CAC included miRNA 497-5p/195 and 106a-5p, and lncRNA FAM197Y7. Top non-coding RNAs revealed significant interplay between genes regulating bone metabolism, vascularization-related processes, chromatin organization, prostaglandin and calcium co-signaling. Prostaglandin E2 receptor 3 (PTGER3), Fibroblasts Growth Factor Receptor 1 (FGFR1), and One Cut Homeobox 2 (ONECUT2) were identified as the most susceptible to regulation by the top non-coding RNAs. This study provides a flexible transcriptomic framework including non-coding regulation for biomarker-related studies.
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Dubaisi S, Fang H, Caruso JA, Gaedigk R, Vyhlidal CA, Kocarek TA, Runge-Morris M. Developmental Expression of SULT1C4 Transcript Variants in Human Liver: Implications for Discordance Between SULT1C4 mRNA and Protein Levels. Drug Metab Dispos 2020; 48:515-520. [PMID: 32303576 DOI: 10.1124/dmd.120.090829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/20/2020] [Indexed: 01/11/2023] Open
Abstract
The cytosolic sulfotransferases (SULTs) metabolize a variety of xenobiotic and endogenous substrates. Several SULTs are expressed in the fetus, implying that these enzymes have important functions during human development. We recently reported that while SULT1C4 mRNA is abundant in prenatal human liver specimens, SULT1C4 protein is barely detectable. Two coding transcript variants (TVs) of SULT1C4 are indexed in GenBank, TV1 (full-length) and TV2 (lacking exons 3 and 4). The purpose of this study was to evaluate expression of the individual TVs as a clue for understanding the discordance between mRNA and protein levels. Reverse-transcription polymerase chain reaction was initially performed to identify TVs expressed in intestinal and hepatic cell lines. This analysis generated fragments corresponding to TV1, TV2, and a third variant that lacked exon 3 (E3DEL). Using reverse-transcription quantitative polymerase chain reaction assays designed to quantify TV1, TV2, or E3DEL individually, all three TVs were more highly expressed in prenatal than postnatal specimens. TV2 levels were ∼fivefold greater than TV1, while E3DEL levels were minimal. RNA sequencing (RNA-seq) analysis of another set of liver specimens confirmed that TV1 and TV2 levels were highest in prenatal liver, with TV2 higher than TV1. RNA-seq also detected a noncoding RNA, which was also more abundant in prenatal liver. Transfection of HEK293T cells with plasmids expressing individual Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys-tagged SULT1C4 isoforms demonstrated that TV1 produced much more protein than did TV2. These data suggest that the lack of correspondence between SULT1C4 mRNA and protein levels in human liver is likely attributable to the inability of the more abundant TV2 to produce stable protein. SIGNIFICANCE STATEMENT: Cytosolic sulfotransferases (SULTs) metabolize a variety of xenobiotic and endogenous substrates, and several SULTs are highly expressed in the fetus, implying that they have important functions during human development. SULT1C4 is highly expressed in prenatal liver at the mRNA level but not the protein level. This study provides an explanation for this discordance by demonstrating that the predominant SULT1C4 transcript is a variant that produces relatively little protein.
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Affiliation(s)
- Sarah Dubaisi
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Hailin Fang
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Joseph A Caruso
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Roger Gaedigk
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Carrie A Vyhlidal
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Thomas A Kocarek
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
| | - Melissa Runge-Morris
- Department of Pharmacology (S.D.) and Institute of Environmental Health Sciences (H.F., J.A.C., T.A.K., M.R.-M.), Wayne State University, Detroit, Michigan; and Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri (R.G., C.A.V.)
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9
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Marco-Puche G, Lois S, Benítez J, Trivino JC. RNA-Seq Perspectives to Improve Clinical Diagnosis. Front Genet 2019; 10:1152. [PMID: 31781178 PMCID: PMC6861419 DOI: 10.3389/fgene.2019.01152] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/22/2019] [Indexed: 01/22/2023] Open
Abstract
In recent years, high-throughput next-generation sequencing technology has allowed a rapid increase in diagnostic capacity and precision through different bioinformatics processing algorithms, tools, and pipelines. The identification, annotation, and classification of sequence variants within different target regions are now considered a gold standard in clinical genetic diagnosis. However, this procedure lacks the ability to link regulatory events such as differential splicing to diseases. RNA-seq is necessary in clinical routine in order to interpret and detect among others splicing events and splicing variants, as it would increase the diagnostic rate by up to 10-35%. The transcriptome has a very dynamic nature, varying according to tissue type, cellular conditions, and environmental factors that may affect regulatory events such as splicing and the expression of genes or their isoforms. RNA-seq offers a robust technical analysis of this complexity, but it requires a profound knowledge of computational/statistical tools that may need to be adjusted depending on the disease under study. In this article we will cover RNA-seq analyses best practices applied to clinical routine, bioinformatics procedures, and present challenges of this approach.
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Affiliation(s)
| | - Sergio Lois
- Bioinformatics Group, Sistemas Genómicos, Paterna, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center, Madrid, Spain
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10
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Hur K, Kim SH, Kim JM. Potential Implications of Long Noncoding RNAs in Autoimmune Diseases. Immune Netw 2019; 19:e4. [PMID: 30838159 PMCID: PMC6399094 DOI: 10.4110/in.2019.19.e4] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/13/2019] [Accepted: 02/17/2019] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are non-protein coding RNAs of more than 200 nucleotides in length. Despite the term “noncoding”, lncRNAs have been reported to be involved in gene expression. Accumulating evidence suggests that lncRNAs play crucial roles in the regulation of immune system and the development of autoimmunity. lncRNAs are expressed in various immune cells including T lymphocytes, B lymphocytes, macrophages, neutrophils, dendritic cells, and NK cells, and are also involved in the differentiation and activation of these immune cells. Here, we review recent studies on the role of lncRNAs in immune regulation and the differential expression of lncRNAs in various autoimmune diseases.
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Affiliation(s)
- Keun Hur
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu 41944, Korea
| | - Sang-Hyon Kim
- Division of Rheumatology, Department of Internal Medicine, Keimyung University Dongsan Medical Center, Keimyung University College of Medicine, Daegu 41931, Korea
| | - Ji-Min Kim
- Division of Rheumatology, Department of Internal Medicine, Keimyung University Dongsan Medical Center, Keimyung University College of Medicine, Daegu 41931, Korea
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11
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Karlik E, Gozukirmizi N. Expression analysis of lncRNA AK370814 involved in the barley vitamin B6 salvage pathway under salinity. Mol Biol Rep 2018; 45:1597-1609. [PMID: 30298351 DOI: 10.1007/s11033-018-4289-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023]
Abstract
Long non-coding RNAs (lncRNAs), which are longer than > 200 nt, perform various functions in a variety of important biological processes. The aim of this study is the investigation of relative expression levels of AK372815 putative pyridoxal reductase (PLR) gene and sense lncRNA AK370814 on four barley genotypes (Hasat, Beysehir 99, Konevi 98 and Tarm 92) in response to 150 mM salinity application during 3 days post-germination. Seeds were placed randomly in petri dishes containing (a) only H2O (control), (b) 150 mM NaCl, for 72 h. RNA isolation was carried out using TriPure® reagent from 150 mM salt-treated root and shoot samples. Relative expression levels of AK372815 PLR and sense lncRNA AK370814 were determined by qPCR. Results demonstrated that salinity affected the expression levels of both AK372815 PLR gene and sense lncRNA AK370814 during germination. Although expression levels of AK372815 PLR tended to be down-regulated under salinity, expression levels of sense lncRNA AK370814 were up-regulated. Another goal of this study is improvement of alternative approach to NGS technologies for determination of relative expression levels of sense lncRNAs under particular circumstances. This is the first report that demonstrates a relationship between lncRNA and vitamin B6 salvage pathway.
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Affiliation(s)
- Elif Karlik
- Department of Biotechnology, Istanbul University, 34134, Vezneciler, Istanbul, Turkey.
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics, Istanbul University, 34134, Vezneciler, Istanbul, Turkey.,Department of Molecular Biology and Genetics, İstinye University, 34010, Zeytinburnu, İstanbul, Turkey
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12
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Morris G, Maes M, Murdjeva M, Puri BK. Do Human Endogenous Retroviruses Contribute to Multiple Sclerosis, and if So, How? Mol Neurobiol 2018; 56:2590-2605. [PMID: 30047100 PMCID: PMC6459794 DOI: 10.1007/s12035-018-1255-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/17/2018] [Indexed: 12/24/2022]
Abstract
The gammaretroviral human endogenous retrovirus (HERV) families MRSV/HERV-W and HERV-H (including the closely related HERV-Fc1) are associated with an increased risk of multiple sclerosis (MS). Complete HERV sequences betray their endogenous retroviral origin, with open reading frames in gag, pro, pol and env being flanked by two long terminal repeats containing promoter and enhancer sequences with the capacity to regulate HERV transactivation and the activity of host genes in spite of endogenous epigenetic repression mechanisms. HERV virions, RNA, cDNA, Gag and Env, and antibodies to HERV transcriptional products, have variously been found in the blood and/or brain and/or cerebrospinal fluid of MS patients, with the HERV expression level being associated with disease status. Furthermore, some HERV-associated single nucleotide polymorphisms (SNPs), such as rs662139 T/C in a 3-kb region of Xq22.3 containing a HERV-W env locus, and rs391745, upstream of the HERV-Fc1 locus on the X chromosome, are associated with MS susceptibility, while a negative association has been reported with SNPs in the tripartite motif-containing (TRIM) protein-encoding genes TRIM5 and TRIM22. Factors affecting HERV transcription include immune activation and inflammation, since HERV promoter regions possess binding sites for related transcription factors; oxidative stress, with oxidation of guanine to 8-oxoguanine and conversion of cytosine to 5-hydroxymethylcytosine preventing binding of methyl groups transferred by DNA methyltransferases; oxidative stress also inhibits the activity of deacetylases, thereby favouring the acetylation of histone lysine residues favouring gene expression; interferon beta; natalizumab treatment; impaired epigenetic regulation; and the sex of patients.
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Affiliation(s)
- Gerwyn Morris
- IMPACT Strategic Research Centre, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
| | - Michael Maes
- IMPACT Strategic Research Centre, School of Medicine, Barwon Health, Deakin University, Geelong, Victoria, Australia
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Marianna Murdjeva
- Department of Microbiology and Immunology, Medical University, Plovdiv, Bulgaria
| | - Basant K Puri
- Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK.
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Das A, Samidurai A, Salloum FN. Deciphering Non-coding RNAs in Cardiovascular Health and Disease. Front Cardiovasc Med 2018; 5:73. [PMID: 30013975 PMCID: PMC6036139 DOI: 10.3389/fcvm.2018.00073] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022] Open
Abstract
After being long considered as “junk” in the human genome, non-coding RNAs (ncRNAs) currently represent one of the newest frontiers in cardiovascular disease (CVD) since they have emerged in recent years as potential therapeutic targets. Different types of ncRNAs exist, including small ncRNAs that have fewer than 200 nucleotides, which are mostly known as microRNAs (miRNAs), and long ncRNAs that have more than 200 nucleotides. Recent discoveries on the role of ncRNAs in epigenetic and transcriptional regulation, atherosclerosis, myocardial ischemia/reperfusion (I/R) injury and infarction (MI), adverse cardiac remodeling and hypertrophy, insulin resistance, and diabetic cardiomyopathy prompted vast interest in exploring candidate ncRNAs for utilization as potential therapeutic targets and/or diagnostic/prognostic biomarkers in CVDs. This review will discuss our current knowledge concerning the roles of different types of ncRNAs in cardiovascular health and disease and provide some insight on the cardioprotective signaling pathways elicited by the non-coding genome. We will highlight important basic and clinical breakthroughs that support employing ncRNAs for treatment or early diagnosis of a variety of CVDs, and also depict the most relevant limitations that challenge this novel therapeutic approach.
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Affiliation(s)
- Anindita Das
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Arun Samidurai
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Fadi N Salloum
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, United States
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14
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Liu P, Jin L, Zhao L, Long K, Song Y, Tang Q, Ma J, Wang X, Tang G, Jiang Y, Zhu L, Li X, Li M. Identification of a novel antisense long non-coding RNA PLA2G16-AS that regulates the expression of PLA2G16 in pigs. Gene 2018; 671:78-84. [PMID: 29860067 DOI: 10.1016/j.gene.2018.05.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023]
Abstract
Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules to control gene expression. However, studies on the NATs of pigs are relatively rare. Here, we identified a novel antisense transcript, designated PLA2G16-AS, transcribed from the phospholipase A2 group XVI locus (PLA2G16) in the porcine genome, which is a well-known regulatory molecule of fat deposition. PLA2G16-AS and PLA2G16 were dominantly expressed in porcine adipose tissue, and were differentially expressed between Tibetan pigs and Rongchang pigs. In addition, PLA2G16-AS has a weak sequence conservation among different vertebrates. PLA2G16-AS was also shown to form an RNA-RNA duplex with PLA2G16, and to regulate PLA2G16 expression at the mRNA level. Moreover, the overexpression of PLA2G16-AS increased the stability of PLA2G16 mRNA in porcine cells. We envision that our findings of a NAT for a regulatory gene associated with lipolysis might further our understanding of the molecular regulation of fat deposition.
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Affiliation(s)
- Pengliang Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Lirui Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Keren Long
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yang Song
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Qianzi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jideng Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xun Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China.
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Girimurugan SB, Liu Y, Lung PY, Vera DL, Dennis JH, Bass HW, Zhang J. iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. BMC Bioinformatics 2018; 19:131. [PMID: 29642840 PMCID: PMC5896135 DOI: 10.1186/s12859-018-2140-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/26/2018] [Indexed: 11/16/2022] Open
Abstract
Background Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean values. Despite dozens of algorithms developed to address this problem in genomics research, methods with improved accuracy and speed are still needed to effectively tackle both existing and emerging genomic and epigenomic segmentation problems. Results We designed an efficient algorithm, called iSeg, for segmentation of genomic and epigenomic profiles. iSeg first utilizes dynamic programming to identify candidate segments and test for significance. It then uses a novel data structure based on two coupled balanced binary trees to detect overlapping significant segments and update them simultaneously during searching and refinement stages. Refinement and merging of significant segments are performed at the end to generate the final set of segments. By using an objective function based on the p-values of the segments, the algorithm can serve as a general computational framework to be combined with different assumptions on the distributions of the data. As a general segmentation method, it can segment different types of genomic and epigenomic data, such as DNA copy number variation, nucleosome occupancy, nuclease sensitivity, and differential nuclease sensitivity data. Using simple t-tests to compute p-values across multiple datasets of different types, we evaluate iSeg using both simulated and experimental datasets and show that it performs satisfactorily when compared with some other popular methods, which often employ more sophisticated statistical models. Implemented in C++, iSeg is also very computationally efficient, well suited for large numbers of input profiles and data with very long sequences. Conclusions We have developed an efficient general-purpose segmentation tool and showed that it had comparable or more accurate results than many of the most popular segment-calling algorithms used in contemporary genomic data analysis. iSeg is capable of analyzing datasets that have both positive and negative values. Tunable parameters allow users to readily adjust the statistical stringency to best match the biological nature of individual datasets, including widely or sparsely mapped genomic datasets or those with non-normal distributions. Electronic supplementary material The online version of this article (10.1186/s12859-018-2140-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Yuhang Liu
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Daniel L Vera
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA
| | - Jonathan H Dennis
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL, USA.
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Deveson IW, Brunck ME, Blackburn J, Tseng E, Hon T, Clark TA, Clark MB, Crawford J, Dinger ME, Nielsen LK, Mattick JS, Mercer TR. Universal Alternative Splicing of Noncoding Exons. Cell Syst 2018; 6:245-255.e5. [DOI: 10.1016/j.cels.2017.12.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 10/18/2017] [Accepted: 12/08/2017] [Indexed: 01/31/2023]
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17
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Li H, Chen C, Fan J, Yin Z, Ni L, Cianflone K, Wang Y, Wang DW. Identification of cardiac long non-coding RNA profile in human dilated cardiomyopathy. Cardiovasc Res 2018; 114:747-758. [PMID: 29365080 DOI: 10.1093/cvr/cvy012] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/19/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Huaping Li
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 No. Jiefang Avenue, Wuhan 430030, China
| | - Chen Chen
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 No. Jiefang Avenue, Wuhan 430030, China
| | - Jiahui Fan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 No. Jiefang Avenue, Wuhan 430030, China
| | - Zhongwei Yin
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 No. Jiefang Avenue, Wuhan 430030, China
| | - Li Ni
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 No. Jiefang Avenue, Wuhan 430030, China
| | - Katherine Cianflone
- Centre de Recherche Institut Universitaire de Cardiologie & Pneumologie de Québec, Faculté Médecine, Université Laval, Laval, QC G1V 4G5, Canada
| | - Yan Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 No. Jiefang Avenue, Wuhan 430030, China
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 No. Jiefang Avenue, Wuhan 430030, China
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18
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Yan H, Bombarely A, Xu B, Frazier TP, Wang C, Chen P, Chen J, Hasing T, Cui C, Zhang X, Zhao B, Huang L. siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:208. [PMID: 30061930 PMCID: PMC6058383 DOI: 10.1186/s13068-018-1202-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes. RESULTS We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar 'Alamo' using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development. CONCLUSIONS This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.
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Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | | | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Taylor P. Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Chengran Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Tomas Hasing
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Chenming Cui
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061 USA
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
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19
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Xia JH, Li HL, Li BJ, Gu XH, Lin HR. Acute hypoxia stress induced abundant differential expression genes and alternative splicing events in heart of tilapia. Gene 2017; 639:52-61. [PMID: 28986317 DOI: 10.1016/j.gene.2017.10.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/26/2017] [Accepted: 10/02/2017] [Indexed: 01/10/2023]
Abstract
Hypoxia is one of the critical environmental stressors for fish in aquatic environments. Although accumulating evidences indicate that gene expression is regulated by hypoxia stress in fish, how genes undergoing differential gene expression and/or alternative splicing (AS) in response to hypoxia stress in heart are not well understood. Using RNA-seq, we surveyed and detected 289 differential expressed genes (DEG) and 103 genes that undergo differential usage of exons and splice junctions events (DUES) in heart of a hypoxia tolerant fish, Nile tilapia, Oreochromis niloticus following 12h hypoxic treatment. The spatio-temporal expression analysis validated the significant association of differential exon usages in two randomly selected DUES genes (fam162a and ndrg2) in 5 tissues (heart, liver, brain, gill and spleen) sampled at three time points (6h, 12h, and 24h) under acute hypoxia treatment. Functional analysis significantly associated the differential expressed genes with the categories related to energy conservation, protein synthesis and immune response. Different enrichment categories were found between the DEG and DUES dataset. The Isomerase activity, Oxidoreductase activity, Glycolysis and Oxidative stress process were significantly enriched for the DEG gene dataset, but the Structural constituent of ribosome and Structural molecule activity, Ribosomal protein and RNA binding protein were significantly enriched only for the DUES genes. Our comparative transcriptomic analysis reveals abundant stress responsive genes and their differential regulation function in the heart tissues of Nile tilapia under acute hypoxia stress. Our findings will facilitate future investigation on transcriptome complexity and AS regulation during hypoxia stress in fish.
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Affiliation(s)
- Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Hong Lian Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
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20
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Transcriptional and Post-transcriptional Gene Regulation by Long Non-coding RNA. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:177-186. [PMID: 28529100 PMCID: PMC5487525 DOI: 10.1016/j.gpb.2016.12.005] [Citation(s) in RCA: 601] [Impact Index Per Article: 85.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/08/2016] [Accepted: 12/25/2016] [Indexed: 02/08/2023]
Abstract
Advances in genomics technology over recent years have led to the surprising discovery that the genome is far more pervasively transcribed than was previously appreciated. Much of the newly-discovered transcriptome appears to represent long non-coding RNA (lncRNA), a heterogeneous group of largely uncharacterised transcripts. Understanding the biological function of these molecules represents a major challenge and in this review we discuss some of the progress made to date. One major theme of lncRNA biology seems to be the existence of a network of interactions with microRNA (miRNA) pathways. lncRNA has been shown to act as both a source and an inhibitory regulator of miRNA. At the transcriptional level, a model is emerging whereby lncRNA bridges DNA and protein by binding to chromatin and serving as a scaffold for modifying protein complexes. Such a mechanism can bridge promoters to enhancers or enhancer-like non-coding genes by regulating chromatin looping, as well as conferring specificity on histone modifying complexes by directing them to specific loci.
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21
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Facella P, Carbone F, Placido A, Perrotta G. Cryptochrome 2 extensively regulates transcription of the chloroplast genome in tomato. FEBS Open Bio 2017; 7:456-471. [PMID: 28396831 PMCID: PMC5377390 DOI: 10.1002/2211-5463.12082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/26/2016] [Accepted: 05/03/2016] [Indexed: 11/07/2022] Open
Abstract
Light plays a key role in the regulation of many physiological processes required for plant and chloroplast development. Plant cryptochromes (crys) play an important role in monitoring, capturing, and transmitting the light stimuli. In this study, we analyzed the effects of CRY2 overexpression on transcription of tomato chloroplast genome by a tiling array, containing about 90 000 overlapping probes (5‐nucleotide resolution). We profiled transcription in leaves of wild‐type and CRY2‐overexpressing plants grown in a diurnal cycle, to generate a comprehensive map of chloroplast transcription and to monitor potential specific modulations of the chloroplast transcriptome induced by the overexpression of CRY2. Our results demonstrate that CRY2 is a master gene of transcriptional regulation in the tomato chloroplast. In fact, it modulates the day/night mRNA abundance of about 58% of the 114 ORFs. The effect of CRY2 includes a differential extension of some transcripts at their 5′‐end, according to the period of the day. We observed that the influence of CRY2 on chloroplast transcription is not limited to coding RNA; a great number of putative noncoding micro RNA also showed differential accumulation pattern. To our knowledge, this is the first study that highlights how a photoreceptor affects the day/night transcription of the chloroplast genome.
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Affiliation(s)
| | - Fabrizio Carbone
- Council for Agricultural Research and Economics The Olive Growing and Olive Product Industry Research Centre Rende (CS) Italy
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22
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Bottini S, Del Tordello E, Fagnocchi L, Donati C, Muzzi A. PIPE-chipSAD: A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes. Front Mol Biosci 2017; 3:82. [PMID: 28066774 PMCID: PMC5167695 DOI: 10.3389/fmolb.2016.00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/30/2016] [Indexed: 11/13/2022] Open
Abstract
PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions. Finally, the pipeline includes anno-chipSAD a method to annotate the detected transcripts in comparison to the genome annotation. Overall, our pipeline allows transcriptional profile analysis of both coding and non-coding portions of the chromosome in a single framework. Importantly, due to its versatile characteristics, it will be of wide applicability to analyse, not only microarray signals, but also data from other high throughput technologies such as RNA-sequencing. The current PIPE-chipSAD implementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD.
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Affiliation(s)
| | | | | | - Claudio Donati
- Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
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Abstract
Long noncoding RNAs (lncRNAs) are nonprotein coding transcripts longer than 200 nucleotides. Many of these lncRNAs have regulatory functions and have recently emerged as major players in governing fundamental biological processes. Here, we review the definition, distribution, identification, databases, analysis, classification, and functions of lncRNAs. We also discuss the potential roles of lncRNAs in the etiological processes of psychiatric disorders and the implications for clinical diagnosis and treatment.
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24
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Strategies to identify natural antisense transcripts. Biochimie 2017; 132:131-151. [DOI: 10.1016/j.biochi.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
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25
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Yang W, Li D, Wang G, Zhang C, Zhang M, Zhang W, Li S. Three intronic lncRNAs with monoallelic expression derived from the MEG8 gene in cattle. Anim Genet 2016; 48:272-277. [PMID: 27925264 DOI: 10.1111/age.12527] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 12/13/2022]
Abstract
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Antisense lncRNAs, intergenetic lncRNAs and enhancer lncRNAs can regulate genomic imprinting, which leads to parent-origin-specific monoalletic expression of genes. However, the function of intronic ncRNAs in genomic imprinting remains unclear. Previously, we obtained the cDNA sequence of cattle MEG8 gene, which is located in the DLK1-DIO3 imprinted clusters of cattle chromosome 21. In this study, we undertook a systematic search for transcripts mapping to the MEG8 intronic region and identified three novel lncRNAs, named MEG8 intronic RNA 1 (MEG8-IT1), MEG8 intronic RNA 2 (MEG8-IT2) and MEG8 intronic RNA 3 (MEG8-IT3) according to the GENCODE annotated bibliography. We characterized the expression pattern of these lncRNAs using RT-PCR in adult cattle tissues, and they were expressed in all tested eight tissues, similar to the expression pattern of MEG8. The allele-specific expression of three novel lncRNAs was assessed using a polymorphism-based sequencing approach. Three single nucleotide polymorphism sites were identified in these three lncRNAs. We found that the three lncRNAs showed monoallelic expression in the analyzed tissues, suggesting that they may be imprinted in cattle. These results expand the number of known monoallelically expressed lncRNAs from the DLK1-DIO3 domain and contribute to further investigation of lncRNA regulatory mechanisms and function.
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Affiliation(s)
- W Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - D Li
- College of Life Science and Life Engineering, Hebei Science and Technology University, Shijiazhuang, 050018, China
| | - G Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - C Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - M Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - W Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - S Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
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Dang Y, Cheng J, Sun X, Zhou Z, Liu Y. Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing. Genes Dev 2016; 30:2417-2432. [PMID: 27856616 PMCID: PMC5131781 DOI: 10.1101/gad.285791.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022]
Abstract
In this study, Dang et al. use Neurospora to demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism. In eukaryotes, antisense transcription can regulate sense transcription by induction of epigenetic modifications. We showed previously that antisense transcription triggers Dicer-independent siRNA (disiRNA) production and disiRNA locus DNA methylation (DLDM) in Neurospora crassa. Here we show that the conserved exonuclease ERI-1 (enhanced RNAi-1) is a critical component in this process. Antisense transcription and ERI-1 binding to target RNAs are necessary and sufficient to trigger DLDM. Convergent transcription causes stalling of RNA polymerase II during transcription, which permits ERI-1 to bind nascent RNAs in the nucleus and recruit a histone methyltransferase complex that catalyzes chromatin modifications. Furthermore, we show that, in the cytoplasm, ERI-1 targets hundreds of transcripts from loci without antisense transcription to regulate RNA stability. Together, our results demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism.
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Affiliation(s)
- Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Beijing 100080, China
| | - Zhipeng Zhou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Mazaki-Tovi S, Tarca AL, Vaisbuch E, Kusanovic JP, Than NG, Chaiworapongsa T, Dong Z, Hassan SS, Romero R. Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition. J Perinat Med 2016; 44:813-835. [PMID: 26994472 PMCID: PMC5987212 DOI: 10.1515/jpm-2015-0259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/26/2015] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The aim of this study was to determine gene expression and splicing changes associated with parturition and regions (visceral vs. subcutaneous) of the adipose tissue of pregnant women. STUDY DESIGN The transcriptome of visceral and abdominal subcutaneous adipose tissue from pregnant women at term with (n=15) and without (n=25) spontaneous labor was profiled with the Affymetrix GeneChip Human Exon 1.0 ST array. Overall gene expression changes and the differential exon usage rate were compared between patient groups (unpaired analyses) and adipose tissue regions (paired analyses). Selected genes were tested by quantitative reverse transcription-polymerase chain reaction. RESULTS Four hundred and eighty-two genes were differentially expressed between visceral and subcutaneous fat of pregnant women with spontaneous labor at term (q-value <0.1; fold change >1.5). Biological processes enriched in this comparison included tissue and vasculature development as well as inflammatory and metabolic pathways. Differential splicing was found for 42 genes [q-value <0.1; differences in Finding Isoforms using Robust Multichip Analysis scores >2] between adipose tissue regions of women not in labor. Differential exon usage associated with parturition was found for three genes (LIMS1, HSPA5, and GSTK1) in subcutaneous tissues. CONCLUSION We show for the first time evidence of implication of mRNA splicing and processing machinery in the subcutaneous adipose tissue of women in labor compared to those without labor.
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Affiliation(s)
- Shali Mazaki-Tovi
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel Hashomer, Israel
- Tel Aviv University, Tel Aviv, Israel
| | - Adi L. Tarca
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Edi Vaisbuch
- Department of Obstetrics and Gynecology, Kaplan Medical Center, Rehovot, Israel
| | - Juan Pedro Kusanovic
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Research and Innovation in Maternal-Fetal Medicine (CIMAF). Department of Obstetrics and Gynecology, Sótero del Río Hospital, Santiago, Chile
| | - Nandor Gabor Than
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Zhong Dong
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Sonia S Hassan
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
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Smith C, Stringer AM, Mao C, Palumbo MJ, Wade JT. Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion. mBio 2016; 7:e01024-16. [PMID: 27601571 PMCID: PMC5013294 DOI: 10.1128/mbio.01024-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/10/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Salmonella enterica pathogenicity island 1 (SPI-1) encodes proteins required for invasion of gut epithelial cells. The timing of invasion is tightly controlled by a complex regulatory network. The transcription factor (TF) HilD is the master regulator of this process and senses environmental signals associated with invasion. HilD activates transcription of genes within and outside SPI-1, including six other TFs. Thus, the transcriptional program associated with host cell invasion is controlled by at least 7 TFs. However, very few of the regulatory targets are known for these TFs, and the extent of the regulatory network is unclear. In this study, we used complementary genomic approaches to map the direct regulatory targets of all 7 TFs. Our data reveal a highly complex and interconnected network that includes many previously undescribed regulatory targets. Moreover, the network extends well beyond the 7 TFs, due to the inclusion of many additional TFs and noncoding RNAs. By comparing gene expression profiles of regulatory targets for the 7 TFs, we identified many uncharacterized genes that are likely to play direct roles in invasion. We also uncovered cross talk between SPI-1 regulation and other regulatory pathways, which, in turn, identified gene clusters that likely share related functions. Our data are freely available through an intuitive online browser and represent a valuable resource for the bacterial research community. IMPORTANCE Invasion of epithelial cells is an early step during infection by Salmonella enterica and requires secretion of specific proteins into host cells via a type III secretion system (T3SS). Most T3SS-associated proteins required for invasion are encoded in a horizontally acquired genomic locus known as Salmonella pathogenicity island 1 (SPI-1). Multiple regulators respond to environmental signals to ensure appropriate timing of SPI-1 gene expression. In particular, there are seven transcription regulators that are known to be involved in coordinating expression of SPI-1 genes. We have used complementary genome-scale approaches to map the gene targets of these seven regulators. Our data reveal a highly complex and interconnected regulatory network that includes many previously undescribed target genes. Moreover, our data functionally implicate many uncharacterized genes in the invasion process and reveal cross talk between SPI-1 regulation and other regulatory pathways. All datasets are freely available through an intuitive online browser.
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Affiliation(s)
- Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Anne M Stringer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Chunhong Mao
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, USA
| | - Michael J Palumbo
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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Abstract
Arraystar LncRNA microarrays are designed for global gene expression profiling of both LncRNAs and mRNAs on the same array. The array contents feature comprehensive collections of LncRNAs and include entire sets of known coding mRNAs. Each RNA transcript is detected by a splice junction-specific probe or a unique exon sequence, such that the alternatively spliced transcript isoforms or variants are reliably and accurately detected. The highly optimized experimental protocols and efficient workflow ensure sensitive, robust, and accurate microarray data generation. Standard data analyses are provided for microarray raw data processing, data quality control, gene expression clustering and heat map visualization, differentially expressed LncRNAs and mRNAs, LncRNA subcategories, regulatory relationships of LncRNAs with the mRNAs, gene ontology, and pathway analysis. The LncRNA microarrays are powerful tools for the study of LncRNAs in biology and disease, with broad applications in gene expression profiling, gene regulatory mechanism research, LncRNA functional discovery, and biomarker development.
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Mazaki-Tovi S, Vaisbuch E, Tarca AL, Kusanovic JP, Than NG, Chaiworapongsa T, Dong Z, Hassan SS, Romero R. Characterization of Visceral and Subcutaneous Adipose Tissue Transcriptome and Biological Pathways in Pregnant and Non-Pregnant Women: Evidence for Pregnancy-Related Regional-Specific Differences in Adipose Tissue. PLoS One 2015; 10:e0143779. [PMID: 26636677 PMCID: PMC4670118 DOI: 10.1371/journal.pone.0143779] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 11/08/2015] [Indexed: 12/13/2022] Open
Abstract
Objective The purpose of this study was to compare the transcriptome of visceral and subcutaneous adipose tissues between pregnant and non-pregnant women. Study Design The transcriptome of paired visceral and abdominal subcutaneous adipose tissues from pregnant women at term and matched non-pregnant women (n = 11) was profiled with the Affymetrix Human Exon 1.0 ST array. Differential expression of selected genes was validated with the use of quantitative reverse transcription–polymerase chain reaction. Results Six hundred forty-four transcripts from 633 known genes were differentially expressed (false discovery rate (FDR) <0.1; fold-change >1.5), while 42 exons from 36 genes showed differential usage (difference in FIRMA scores >2 and FDR<0.1) between the visceral and subcutaneous fat of pregnant women. Fifty-six known genes were differentially expressed between pregnant and non-pregnant subcutaneous fat and three genes in the visceral fat. Enriched biological processes in the subcutaneous adipose tissue of pregnant women were mostly related to inflammation. Conclusion The transcriptome of visceral and subcutaneous fat depots reveals pregnancy-related gene expression and splicing differences in both visceral and subcutaneous adipose tissue. Furthermore, for the first time, alternative splicing in adipose tissue has been associated with regional differences and human parturition.
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Affiliation(s)
- Shali Mazaki-Tovi
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel Hashomer, Israel
- Tel Aviv University, Tel Aviv, Israel
- * E-mail: (SMT); (RR)
| | - Edi Vaisbuch
- Department of Obstetrics and Gynecology, Kaplan Medical Center, Rehovot, Israel
| | - Adi L. Tarca
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Juan Pedro Kusanovic
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Research and Innovation in Maternal-Fetal Medicine (CIMAF), Department of Obstetrics and Gynecology, Sótero del Río Hospital, Santiago, Chile
| | - Nandor Gabor Than
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Zhong Dong
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Sonia S. Hassan
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail: (SMT); (RR)
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Taylor DH, Chu ETJ, Spektor R, Soloway PD. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev 2015; 82:932-56. [PMID: 26517592 PMCID: PMC4762656 DOI: 10.1002/mrd.22581] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have long been known to play vital roles in eukaryotic gene regulation. Studies conducted over a decade ago revealed that maturation of spliced, polyadenylated coding mRNA occurs by reactions involving small nuclear RNAs and small nucleolar RNAs; mRNA translation depends on activities mediated by transfer RNAs and ribosomal RNAs, subject to negative regulation by micro RNAs; transcriptional competence of sex chromosomes and some imprinted genes is regulated in cis by ncRNAs that vary by species; and both small-interfering RNAs and piwi-interacting RNAs bound to Argonaute-family proteins regulate post-translational modifications on chromatin and local gene expression states. More recently, gene-regulating noncoding RNAs have been identified, such as long intergenic and long noncoding RNAs (collectively referred to as lncRNAs)--a class totaling more than 100,000 transcripts in humans, which include some of the previously mentioned RNAs that regulate dosage compensation and imprinted gene expression. Here, we provide an overview of lncRNA activities, and then review the role of lncRNAs in processes vital to reproduction, such as germ cell specification, sex determination and gonadogenesis, sex hormone responses, meiosis, gametogenesis, placentation, non-genetic inheritance, and pathologies affecting reproductive tissues. Results from many species are presented to illustrate the evolutionarily conserved processes lncRNAs are involved in.
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Affiliation(s)
- David H. Taylor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Erin Tsi-Jia Chu
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
| | - Roman Spektor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Paul D. Soloway
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
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Role of the Neuregulin Signaling Pathway in Nicotine Dependence and Co-morbid Disorders. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 124:113-31. [PMID: 26472527 DOI: 10.1016/bs.irn.2015.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Smoking is currently the leading cause of preventable death in the United States and is responsible for over four million deaths annually worldwide. Therefore, there is a vast clinical unmet need with regards to therapeutics targeting smoking cessation. This is even more apparent when examining smokers co-morbid with psychiatric illness, as rates of smoking in this population are ~4× higher than in the general population. Examining common genetic and molecular signaling pathways impinging upon both smoking behavior and psychiatric illness will lead to a better understanding of co-morbid disorders and potential development of novel therapeutics. Studies have implicated the Neuregulin Signaling Pathway in the pathophysiology of a number of psychiatric illnesses. Additionally, recent studies have also shown an association between the Neuregulin Signaling Pathway and smoking behaviors. This review outlines basic mechanisms of the Neuregulin Signaling Pathway and how it may be exploited for precision medicine approaches in treating nicotine dependence and mental illness.
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Brečević L, Rinčić M, Krsnik Ž, Sedmak G, Hamid AB, Kosyakova N, Galić I, Liehr T, Borovečki F. Association of new deletion/duplication region at chromosome 1p21 with intellectual disability, severe speech deficit and autism spectrum disorder-like behavior: an all-in approach to solving the DPYD enigma. Transl Neurosci 2015; 6:59-86. [PMID: 28123791 PMCID: PMC4936614 DOI: 10.1515/tnsci-2015-0007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/29/2014] [Indexed: 12/14/2022] Open
Abstract
We describe an as yet unreported neocentric small supernumerary marker chromosome (sSMC) derived from chromosome 1p21.3p21.2. It was present in 80% of the lymphocytes in a male patient with intellectual disability, severe speech deficit, mild dysmorphic features, and hyperactivity with elements of autism spectrum disorder (ASD). Several important neurodevelopmental genes are affected by the 3.56 Mb copy number gain of 1p21.3p21.2, which may be considered reciprocal in gene content to the recently recognized 1p21.3 microdeletion syndrome. Both 1p21.3 deletions and the presented duplication display overlapping symptoms, fitting the same disorder category. Contribution of coding and non-coding genes to the phenotype is discussed in the light of cellular and intercellular homeostasis disequilibrium. In line with this the presented 1p21.3p21.2 copy number gain correlated to 1p21.3 microdeletion syndrome verifies the hypothesis of a cumulative effect of the number of deregulated genes - homeostasis disequilibrium leading to overlapping phenotypes between microdeletion and microduplication syndromes. Although miR-137 appears to be the major player in the 1p21.3p21.2 region, deregulation of the DPYD (dihydropyrimidine dehydrogenase) gene may potentially affect neighboring genes underlying the overlapping symptoms present in both the copy number loss and copy number gain of 1p21. Namely, the all-in approach revealed that DPYD is a complex gene whose expression is epigenetically regulated by long non-coding RNAs (lncRNAs) within the locus. Furthermore, the long interspersed nuclear element-1 (LINE-1) L1MC1 transposon inserted in DPYD intronic transcript 1 (DPYD-IT1) lncRNA with its parasites, TcMAR-Tigger5b and pair of Alu repeats appears to be the “weakest link” within the DPYD gene liable to break. Identification of the precise mechanism through which DPYD is epigenetically regulated, and underlying reasons why exactly the break (FRA1E) happens, will consequently pave the way toward preventing severe toxicity to the antineoplastic drug 5-fluorouracil (5-FU) and development of the causative therapy for the dihydropyrimidine dehydrogenase deficiency.
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Affiliation(s)
- Lukrecija Brečević
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- E-mail: ;
| | - Martina Rinčić
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Željka Krsnik
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Goran Sedmak
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Ahmed B. Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Ivan Galić
- Center for Rehabilitation Stančić, Stančić bb, 10370 Stančić, Croatia
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
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Kianianmomeni A, Ong CS, Rätsch G, Hallmann A. Genome-wide analysis of alternative splicing in Volvox carteri. BMC Genomics 2014; 15:1117. [PMID: 25516378 PMCID: PMC4378016 DOI: 10.1186/1471-2164-15-1117] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/11/2014] [Indexed: 11/15/2022] Open
Abstract
Background Alternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Particularly in multicellular eukaryotes, this mechanism is involved in the regulation of developmental and physiological processes like growth, differentiation and signal transduction. Results Here we report the genome-wide analysis of alternative splicing in the multicellular green alga Volvox carteri. The bioinformatic analysis of 132,038 expressed sequence tags (ESTs) identified 580 alternative splicing events in a total of 426 genes. The predominant type of alternative splicing in Volvox is intron retention (46.5%) followed by alternative 5′ (17.9%) and 3′ (21.9%) splice sites and exon skipping (9.5%). Our analysis shows that in Volvox at least ~2.9% of the intron-containing genes are subject to alternative splicing. Considering the total number of sequenced ESTs, the Volvox genome seems to provide more favorable conditions (e.g., regarding length and GC content of introns) for the occurrence of alternative splicing than the genome of its close unicellular relative Chlamydomonas. Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas. Since the Volvox genome contains about the same number of protein-coding genes as the Chlamydomonas genome (~14,500 protein-coding genes), we assumed that alternative splicing may play a key role in generation of genomic diversity, which is required to evolve from a simple one-cell ancestor to a multicellular organism with differentiated cell types (Mol Biol Evol 31:1402-1413, 2014). To confirm the alternative splicing events identified by bioinformatic analysis, several genes with different types of alternatively splicing have been selected followed by experimental verification of the predicted splice variants by RT-PCR. Conclusions The results show that our approach for prediction of alternative splicing events in Volvox was accurate and reliable. Moreover, quantitative real-time RT-PCR appears to be useful in Volvox for analyses of relationships between the appearance of specific alternative splicing variants and different kinds of physiological, metabolic and developmental processes as well as responses to environmental changes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1117) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr, 25, D-33615 Bielefeld, Germany.
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Rahmati S, Emadi-Baygi M, Nikpour P, Emadi-Andani E. Expression profile of ZFX isoform3/variant 5 in gastric cancer tissues and its association with tumor size. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2014; 17:767-71. [PMID: 25729545 PMCID: PMC4340984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/15/2014] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Previous studies demonstrate that changes in pre-mRNA splicing play a significant role in human disease development. Furthermore, many cancer-associated genes are regulated by alternative splicing. There are mounting evidences that splice variants which express predominantly in tumors, have clear diagnostic value and may provide potential drug targets. Located on the X chromosome, ZFX gene functions as a transcription regulator for self-renewal of stem cells. This gene has 5 splice variants that encode 3 isoforms. In the present study, we evaluated the clinicopathological relevance of the expression of ZFX isoform 3/variant 5 gene in gastric carcinoma. MATERIALS AND METHODS A total of 60 tumoral and non-tumoral gastric specimens were evaluated for ZFX isoform 3/variant 5 gene expression using quantitative real-time PCR. RESULTS Our results showed that the expression of ZFX isoform 3/variant 5 transcript was heterogeneous in gastric specimens. We further showed that there was a positive correlation between the variant expression and tumor size, but not with other clinicopathological features of gastric tumors. CONCLUSION This report shows that the expression of ZFX isoform 3/variant 5 transcript was heterogeneous in gastric specimens. Furthermore, there was no significant association between ZFX isoform 3/variant 5 expression and most of clinicopathological features of gastric tumors except for a positive correlation with tumor size. The elucidation of the precise molecular mechanisms governed by the ZFX isoforms/variants needs further investigation.
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Affiliation(s)
- Shima Rahmati
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran,Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Parvaneh Nikpour
- Pediatric Inherited Diseases Research Center,Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran,Child Growth and Development Research Center, Isfahan University of Medical Sciences, Isfahan, Iran,Corresponding author: Parvaneh Nikpour, Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran. Tel: +98 31 37922423; Fax: +98 31 37753480;
| | - Elaheh Emadi-Andani
- Child Growth and Development Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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Clark BS, Blackshaw S. Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. Front Genet 2014; 5:164. [PMID: 24936207 PMCID: PMC4047558 DOI: 10.3389/fgene.2014.00164] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/18/2014] [Indexed: 01/17/2023] Open
Abstract
Comprehensive analysis of the mammalian transcriptome has revealed that long non-coding RNAs (lncRNAs) may make up a large fraction of cellular transcripts. Recent years have seen a surge of studies aimed at functionally characterizing the role of lncRNAs in development and disease. In this review, we discuss new findings implicating lncRNAs in controlling development of the central nervous system (CNS). The evolution of the higher vertebrate brain has been accompanied by an increase in the levels and complexities of lncRNAs expressed within the developing nervous system. Although a limited number of CNS-expressed lncRNAs are now known to modulate the activity of proteins important for neuronal differentiation, the function of the vast majority of neuronal-expressed lncRNAs is still unknown. Topics of intense current interest include the mechanism by which CNS-expressed lncRNAs might function in epigenetic and transcriptional regulation during neuronal development, and how gain and loss of function of individual lncRNAs contribute to neurological diseases.
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Affiliation(s)
- Brian S Clark
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Seth Blackshaw
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Ophthalmology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Neurology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Center for High-Throughput Biology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Institute for Cell Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
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Abstract
The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non-protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.
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Hackermüller J, Reiche K, Otto C, Hösler N, Blumert C, Brocke-Heidrich K, Böhlig L, Nitsche A, Kasack K, Ahnert P, Krupp W, Engeland K, Stadler PF, Horn F. Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. Genome Biol 2014; 15:R48. [PMID: 24594072 PMCID: PMC4054595 DOI: 10.1186/gb-2014-15-3-r48] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 03/04/2014] [Indexed: 12/16/2022] Open
Abstract
Background The genome is pervasively transcribed but most transcripts do not code for proteins, constituting non-protein-coding RNAs. Despite increasing numbers of functional reports of individual long non-coding RNAs (lncRNAs), assessing the extent of functionality among the non-coding transcriptional output of mammalian cells remains intricate. In the protein-coding world, transcripts differentially expressed in the context of processes essential for the survival of multicellular organisms have been instrumental in the discovery of functionally relevant proteins and their deregulation is frequently associated with diseases. We therefore systematically identified lncRNAs expressed differentially in response to oncologically relevant processes and cell-cycle, p53 and STAT3 pathways, using tiling arrays. Results We found that up to 80% of the pathway-triggered transcriptional responses are non-coding. Among these we identified very large macroRNAs with pathway-specific expression patterns and demonstrated that these are likely continuous transcripts. MacroRNAs contain elements conserved in mammals and sauropsids, which in part exhibit conserved RNA secondary structure. Comparing evolutionary rates of a macroRNA to adjacent protein-coding genes suggests a local action of the transcript. Finally, in different grades of astrocytoma, a tumor disease unrelated to the initially used cell lines, macroRNAs are differentially expressed. Conclusions It has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events.
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Li J, Kannan M, Trivett AL, Liao H, Wu X, Akagi K, Symer DE. An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition. Nucleic Acids Res 2014; 42:4546-62. [PMID: 24493738 PMCID: PMC3985663 DOI: 10.1093/nar/gku091] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Between 6 and 30% of human and mouse transcripts are initiated from transposable elements. However, the promoters driving such transcriptional activity are mostly unknown. We experimentally characterized an antisense (AS) promoter in mouse L1 retrotransposons for the first time, oriented antiparallel to the coding strand of L1 open reading frame-1. We found that AS transcription is mediated by RNA polymerase II. Rapid amplification of cDNA ends cloning mapped transcription start sites adjacent to the AS promoter. We identified >100 novel fusion transcripts, of which many were conserved across divergent mouse lineages, suggesting conservation of potential functions. To evaluate whether AS L1 transcription could regulate L1 retrotransposition, we replaced portions of native open reading frame-1 in donor elements by synonymously recoded sequences. The resulting L1 elements lacked AS promoter activity and retrotransposed more frequently than endogenous L1s. Overexpression of AS L1 transcripts also reduced L1 retrotransposition. This suppression of retrotransposition was largely independent of Dicer. Our experiments shed new light on how AS fusion transcripts are initiated from endogenous L1 elements across the mouse genome. Such AS transcription can contribute substantially both to natural transcriptional variation and to endogenous regulation of L1 retrotransposition.
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Affiliation(s)
- Jingfeng Li
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA, Laboratory of Molecular Technology, Advanced Technology Program, SAIC-Frederick, Inc., Frederick, MD 21702, USA, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA, Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA, Internal Medicine, The Ohio State University, Columbus, OH 43210, USA and Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
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Nielsen MM, Tehler D, Vang S, Sudzina F, Hedegaard J, Nordentoft I, Ørntoft TF, Lund AH, Pedersen JS. Identification of expressed and conserved human noncoding RNAs. RNA (NEW YORK, N.Y.) 2014; 20:236-251. [PMID: 24344320 PMCID: PMC3895275 DOI: 10.1261/rna.038927.113] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 11/07/2013] [Indexed: 06/03/2023]
Abstract
The past decade has shown mammalian genomes to be pervasively transcribed and identified thousands of noncoding (nc) transcripts. It is currently unclear to what extent these transcripts are of functional importance, as experimental functional evidence exists for only a small fraction. Here, we characterize the expression and evolutionary conservation properties of 12,115 known and novel nc transcripts, including structural RNAs, long nc RNAs (lncRNAs), antisense RNAs, EvoFold predictions, ultraconserved elements, and expressed nc regions. Expression levels are evaluated across 12 human tissues using a custom-designed microarray, supplemented with RNAseq. Conservation levels are evaluated at both the base level and at the syntenic level. We combine these measures with epigenetic mark annotations to identify subsets of novel nc transcripts that show characteristics similar to known functional ncRNAs. Few novel nc transcripts show both high expression and conservation levels. However, overall, we observe a positive correlation between expression and both conservation and epigenetic annotations, suggesting that a subset of the expressed transcripts are under purifying selection and likely functional. The identified subsets of expressed and conserved novel nc transcripts may form the basis for further functional characterization.
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Affiliation(s)
- Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
| | - Disa Tehler
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Søren Vang
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
| | - Frantisek Sudzina
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
| | - Torben Falck Ørntoft
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
| | - Anders H. Lund
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
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41
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Podshivalova K, Salomon DR. MicroRNA regulation of T-lymphocyte immunity: modulation of molecular networks responsible for T-cell activation, differentiation, and development. Crit Rev Immunol 2014; 33:435-76. [PMID: 24099302 DOI: 10.1615/critrevimmunol.2013006858] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNA) are a class of small non-coding RNAs that constitute an essential and evolutionarily conserved mechanism for post-transcriptional gene regulation. Multiple miRNAs have been described to play key roles in T-lymphocyte development, differentiation, and function. In this review, we highlight the current literature regarding the differential expression of miRNAs in various models of murine and human T-cell biology. We emphasize mechanistic understandings of miRNA regulation of thymocyte development, T-cell activation, and differentiation into effector and memory subsets. We describe the participation of miRNAs in complex regulatory circuits shaping T-cell proteomes in a context-dependent manner. It is striking that some miRNAs regulate multiple processes, while others only appear in limited functional contexts. It is also evident that the expression and function of specific miRNAs can differ between murine and human systems. Ultimately, it is not always correct to simplify the complex events of T-cell biology into a model driven by only one or two master regulator miRNAs. In reality, T-cell activation and differentiation involve the expression of multiple miRNAs with many mRNA targets; thus, the true extent of miRNA regulation of T-cell biology is likely far more vast than currently appreciated.
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Affiliation(s)
- Katie Podshivalova
- Laboratory for Functional Genomics, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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42
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Abstract
As more and more systems biology approaches are used to investigate the different types of biological macromolecules, increasing numbers of whole genomic studies are now available for a large array of organisms. Whether it is genomics, transcriptomics, proteomics, interactomics or metabolomics, the full complement of genomic information on all different levels can be juxtaposed between different organisms to reveal similarities or differences, and even to provide consensus models. At the intersection of comparative genomics and systems biology lies great possibility for discovery, analysis and prediction. This paper explores this nexus and the relationship from four general levels: DNA, RNA, protein and extragenomic. For each level, we provide an overview of the methods, discuss the potential challenges and survey the current research. Finally, we suggest some organizing principles and make proposals for new areas that will be important for future research.
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Affiliation(s)
- Jimmy Lin
- Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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43
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Qian X, Ba Y, Zhuang Q, Zhong G. RNA-Seq technology and its application in fish transcriptomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 18:98-110. [PMID: 24380445 DOI: 10.1089/omi.2013.0110] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.
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Affiliation(s)
- Xi Qian
- 1 Department of Animal Science, University of Vermont , Burlington, Vermont
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44
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Lammens T, D'hont I, D'Herde K, Benoit Y, Diez-Fraile A. Long non-coding RNAs in pluripotent stem cell biology. Vet Q 2013; 33:202-6. [PMID: 24256470 DOI: 10.1080/01652176.2013.866297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Pluripotent stem cells are defined by their unlimited self-renewal capacities and potential to differentiate into any cell lineage. Many crucial determinants for the induction and maintenance of this pluripotent state have been identified. Long non-coding RNAs have recently emerged as key regulators of pluripotent stem cells and have enhanced our understanding of their potential functions in tissue regeneration. This review provides an overview of recent important insights into the roles of long non-coding RNAs as regulators and markers of pluripotency.
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Affiliation(s)
- Tim Lammens
- a Department of Pediatric Hematology-Oncology and Stem Cell Transplantation , Ghent University Hospital, 3K12D , De Pintelaan 185, 9000 Ghent , Belgium
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45
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Abstract
Antisense transcription, which was initially considered by many as transcriptional noise, is increasingly being recognized as an important regulator of gene expression. It is widespread among all kingdoms of life and has been shown to influence - either through the act of transcription or through the non-coding RNA that is produced - almost all stages of gene expression, from transcription and translation to RNA degradation. Antisense transcription can function as a fast evolving regulatory switch and a modular scaffold for protein complexes, and it can 'rewire' regulatory networks. The genomic arrangement of antisense RNAs opposite sense genes indicates that they might be part of self-regulatory circuits that allow genes to regulate their own expression.
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46
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Mathiyalagan P, Keating ST, Du XJ, El-Osta A. Interplay of chromatin modifications and non-coding RNAs in the heart. Epigenetics 2013; 9:101-12. [PMID: 24247090 DOI: 10.4161/epi.26405] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Precisely regulated patterns of gene expression are dependent on the binding of transcription factors and chromatin-associated determinants referred to as co-activators and co-repressors. These regulatory components function with the core transcriptional machinery to serve in critical activities to alter chromatin modification and regulate gene expression. While we are beginning to understand that cell-type specific patterns of gene expression are necessary to achieve selective cardiovascular developmental programs, we still do not know the molecular machineries that localize these determinants in the heart. With clear implications for the epigenetic control of gene expression signatures, the ENCODE (Encyclopedia of DNA Elements) Project Consortium determined that about 90% of the human genome is transcribed while only 1-2% of transcripts encode proteins. Emerging evidence suggests that non-coding RNA (ncRNA) serves as a signal for decoding chromatin modifications and provides a potential molecular basis for cell type-specific and promoter-specific patterns of gene expression. The discovery of the histone methyltransferase enzyme EZH2 in the regulation of gene expression patterns implicated in cardiac hypertrophy suggests a novel role for chromatin-associated ncRNAs and is the focus of this article.
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Affiliation(s)
- Prabhu Mathiyalagan
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Samuel T Keating
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Xiao-Jun Du
- Experimental Cardiology Laboratory; Baker IDI Heart and Diabetes Institute; Melbourne, VIC Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Epigenomics Profiling Facility; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Department of Pathology; The University of Melbourne; Melbourne, VIC Australia; Faculty of Medicine; Monash University; Melbourne, VIC Australia
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47
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Samatov TR, Tonevitsky AG, Schumacher U. Epithelial-mesenchymal transition: focus on metastatic cascade, alternative splicing, non-coding RNAs and modulating compounds. Mol Cancer 2013; 12:107. [PMID: 24053443 PMCID: PMC3848796 DOI: 10.1186/1476-4598-12-107] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 09/16/2013] [Indexed: 12/18/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a key process in embryonic development and metastases formation during malignant progression. This review focuses on transcriptional regulation, non-coding RNAs, alternative splicing events and cell adhesion molecules regulation during EMT. Additionally, we summarize the knowledge with regard to the small potentially druggable molecules capable of modulating EMT for cancer therapy.
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Affiliation(s)
- Timur R Samatov
- SRC Bioclinicum, Ugreshskaya str 2/85, Moscow 115088, Russia.
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48
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Ilott NE, Ponting CP. Predicting long non-coding RNAs using RNA sequencing. Methods 2013; 63:50-9. [PMID: 23541739 DOI: 10.1016/j.ymeth.2013.03.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 02/01/2023] Open
Abstract
The advent of next-generation sequencing, and in particular RNA-sequencing (RNA-seq), technologies has expanded our knowledge of the transcriptional capacity of human and other animal, genomes. In particular, recent RNA-seq studies have revealed that transcription is widespread across the mammalian genome, resulting in a large increase in the number of putative transcripts from both within, and intervening between, known protein-coding genes. Long transcripts that appear to lack protein-coding potential (long non-coding RNAs, lncRNAs) have been the focus of much recent research, in part owing to observations of their cell-type and developmental time-point restricted expression patterns. A variety of sequencing protocols are currently available for identifying lncRNAs including RNA polymerase II occupancy, chromatin state maps and - the focus of this review - deep RNA sequencing. In addition, there are numerous analytical methods available for mapping reads and assembling transcript models that predict the presence and structure of lncRNAs from RNA-seq data. Here we review current methods for identifying lncRNAs using large-scale sequencing data from RNA-seq experiments and highlight analytical considerations that are required when undertaking such projects.
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Affiliation(s)
- Nicholas E Ilott
- CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, UK.
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49
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McHale CM, Zhang L, Thomas R, Smith MT. Analysis of the transcriptome in molecular epidemiology studies. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:500-517. [PMID: 23907930 PMCID: PMC5142298 DOI: 10.1002/em.21798] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/07/2013] [Accepted: 06/08/2013] [Indexed: 05/29/2023]
Abstract
The human transcriptome is complex, comprising multiple transcript types, mostly in the form of non-coding RNA (ncRNA). The majority of ncRNA is of the long form (lncRNA, ≥ 200 bp), which plays an important role in gene regulation through multiple mechanisms including epigenetics, chromatin modification, control of transcription factor binding, and regulation of alternative splicing. Both mRNA and ncRNA exhibit additional variability in the form of alternative splicing and RNA editing. All aspects of the human transcriptome can potentially be dysregulated by environmental exposures. Next-generation RNA sequencing (RNA-Seq) is the best available methodology to measure this although it has limitations, including experimental bias. The third phase of the MicroArray Quality Control Consortium project (MAQC-III), also called Sequencing Quality Control (SeQC), aims to address these limitations through standardization of experimental and bioinformatic methodologies. A limited number of toxicogenomic studies have been conducted to date using RNA-Seq. This review describes the complexity of the human transcriptome, the application of transcriptomics by RNA-Seq or microarray in molecular epidemiology studies, and limitations of these approaches including the type of cell or tissue analyzed, experimental variation, and confounding. By using good study designs with precise, individual exposure measurements, sufficient power and incorporation of phenotypic anchors, studies in human populations can identify biomarkers of exposure and/or early effect and elucidate mechanisms of action underlying associated diseases, even at low doses. Analysis of datasets at the pathway level can compensate for some of the limitations of RNA-Seq and, as more datasets become available, will increasingly elucidate the exposure-disease continuum.
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Affiliation(s)
- Cliona M McHale
- Division of Environmental Health Sciences, Genes and Environment Laboratory, School of Public Health, University of California, Berkeley, California 94720, USA.
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50
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Leviatan N, Alkan N, Leshkowitz D, Fluhr R. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PLoS One 2013; 8:e66511. [PMID: 23776682 PMCID: PMC3679080 DOI: 10.1371/journal.pone.0066511] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 05/10/2013] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.
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Affiliation(s)
- Noam Leviatan
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Alkan
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Biological Services Department, Weizmann Institute of Science, Rehovot, Israel
| | - Robert Fluhr
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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